Assembly and folding of fc-interferon-beta fusion proteins

ABSTRACT

Disclosed are Fc-interferon-beta (Fc-IFN-β) fusion proteins and nucleic acid molecules encoding them. The Fc-IFN-β fusion proteins include variants of the interferon-beta (IFN-β) protein that are altered to achieve enhanced biological activity, prolonged circulating half-life and greater solubility. Also disclosed are methods of producing the fusion proteins and methods of using the fusion proteins and/or nucleic acid molecules for treating diseases and conditions alleviated by the administration of interferon-beta.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims priority to and the benefit of U.S. Provisional Patent Application Ser. No. 60/583,389, filed on Jun. 28, 2004, the entire disclosure of which is incorporated by reference herein.

FIELD OF THE INVENTION

The invention relates to Fc-fusion proteins. More specifically, the invention relates to high-level expression and secretion of Fc-interferon-beta fusion proteins and variant forms thereof, and methods of making and using such proteins.

BACKGROUND OF THE INVENTION

Interferons are single chain polypeptides secreted by most animal cells in response to a variety of stimuli, including viruses, mitogens and cytokines. Interferons participate in the regulation of cell functions and mediate antiproliferative, antiviral and immunomodulatory effects. Thus, they are of great interest therapeutically. Native interferons are divided into three major types, based on the cell types from which they are primarily derived, namely, interferon-α (from leukocytes), interferon-β (from fibroblasts), interferon-γ (from immune cells). Interferon-β (IFN-β) exhibits various biological and immunological activities and as a result has potential applications in immunotherapy, antitumor, anticancer and antiviral therapies. Numerous investigations and clinical trials have been and are being conducted based on anticancer and antiviral properties of both wild-type and recombinant IFN-β. Clinical trials using recombinant IFN-β in the treatment of multiple sclerosis also have been conducted.

Most cytokines, including native IFN-β, have relatively short circulating half-lives. Consequently, in order for IFN-β to be effective as a therapeutic agent, it must be administered in large and frequent doses to a patient; however, this often leads to toxic side effects. Therefore, it is highly desirable to produce forms of IFNβ that have prolonged circulating half-lives compared to the native cytokine. Furthermore, for production purposes it is useful to produce forms of IFN-β that are easy to express and purify in large amounts.

Human IFN-β (huIFN-β) is a glycoprotein of 166 amino acids and has a four helix-bundle structure. Recombinant huIFN-β may be commonly produced for use as a therapeutic in either a prokaryotic or a mammalian expression system. However, when proteins that are normally secreted, such as huIFN-β, in a mammalian environment are produced in a prokaryote, the effect of prokaryotic expression on protein folding and on potential post-translational modifications needs to be addressed. For example, in mammalian cells, most proteins destined for the extracellular milieu are folded in the oxidizing environment of the endoplasmic reticulum (ER), which promotes the correct formation of disulfide bonds. In contrast, the reducing environment of the prokaryotic cytosol interferes with the formation of cysteine bonds. In addition, proteins expressed in prokaryotic systems lack some post-translational modifications, such as N-linked glycosylation, which likely aid in the correct folding of the protein, increase the stability of the folded protein, and decrease the immunogenicity of the administered protein.

For example, when intact wild-type IFN-β is expressed in a prokaryotic expression system, it does not fold properly and forms aggregates. This can be overcome by mutating the free cysteine at position 17 of the mature IFN-β protein to, for example, a serine. This cysteine at position 17 is not involved in a disulfide bond. See, for example, U.S. Pat. No. 4,737,462. In contrast, when intact wild-type IFN-β is produced in a eukaryotic expression system, where the environment is appropriate for correct folding of the IFN-β protein, improper folding and aggregation are not observed. Because IFN-β protein appears to fold properly and not to aggregate when expressed in a eukaryotic expression system, this suggests that glycosylation plays an important role in proper folding of the IFN-β protein. Recombinant IFN-β produced in a eukaryotic expression system undergoes glycosylation, although it may not have the precise glycosylation pattern of the native IFN-β. See, for example, U.S. Pat. No. 5,795,779. Whereas glycosylation of IFN-β does not seem to be essential for its biological activity, the specific activity of glycosylated IFN-β in bioassays is greater than that of the unglycosylated form. Indeed, IFN-β produced in a eukaryotic expression system, such as a mammalian expression system, is substantially non-aggregated, but does form aggregates when the glycan moiety is removed. Therefore, the glycosylated form of IFN-β is desirable for therapeutic use as its biophysical properties are closer to those of the native protein than the unglycosylated form.

In addition, it has been found that linking a protein of interest “X” to an immunoglobulin Fc domain “Fc” to create an Fc-X fusion protein (“immunofusin”) generally has the effect of increasing protein production significantly. This is believed to occur, in part, because the Fc moiety of the fusion protein, commonly referred to as the expression cassette, is designed for efficient secretion of the fusion protein, and in part because proteins are being produced and secreted from mammalian cells that are normally active for secretion. A further advantage of creating Fc-X fusion proteins is that the resultant immunofusins exhibit an increased circulating half-life as compared to the free proteins of interest, which can be a significant therapeutic advantage.

There is, therefore, a need in the art for biologically active immunofusins including an Fc moiety fused to an IFN-β moiety optimized to have biophysical properties that are close to those of native IFN-β.

SUMMARY OF THE INVENTION

The invention provides methods and compositions for expressing soluble, biologically active Fc-IFN-β fusion proteins and variants thereof (Fc-IFN-β^(sol)). The Fc-IFN-β^(sol) fusion proteins of the invention demonstrate improved biological properties over unaltered Fc-IFN-β proteins such as increased solubility, prolonged circulating half-life, enhanced biological activity, and reduced immunogenicity.

To improve the circulating half-life of IFN-β, the invention provides a fusion protein including an Fc-IFN-β fusion protein including an immunoglobulin Fc region and an IFN-β protein linked to the carboxy-terminus of the immunoglobulin Fc region. To improve folding and to reduce aggregation, the IFN-β protein includes an amino acid alteration at at least one of positions 17, 50, 57, 130, 131, 136, and 140, corresponding to native mature interferon-β. The alteration to the amino acid can be a deletion, substitution or modification. In one embodiment, the amino acid alteration substitutes either serine, alanine, valine or methionine in place of cysteine at position 17. In another embodiment, the amino acid alteration substitutes histidine in place of phenylalanine at position 50. In yet another embodiment, the amino acid alteration substitutes alanine in place of leucine at position 57, while in a further embodiment, the amino acid alteration substitutes alanine in place of leucine at position 130. A further embodiment allows an amino acid alteration substituting alanine in place of histidine at position 131, while an additional embodiment contemplates substituting alanine in place of lysine at position 136. In yet another embodiment, the amino acid alteration substitutes alanine or threonine in place of histidine at position 140.

The immunoglobulin Fc region can include an immunoglobulin hinge region and an immunoglobulin heavy chain constant region. In one embodiment, the Fc region is derived from IgG4, while in another it is derived from IgG1, and in yet another it is derived from IgG2. In another embodiment, the Fc region is derived from IgG4 but includes a hinge region from IgG1. In yet another embodiment, the Fc region is derived from IgG2 but includes a hinge region derived from IgG1. When the Fc region includes a CH3 domain, the C-terminal lysine of the immunoglobulin Fc region can be replaced by an alanine residue. In a further embodiment, a cysteine residue of the hinge region is mutated.

The invention provides different methods for joining the Fc moiety and the IFN-β moiety to create fusion proteins according to the invention. For example, in one embodiment the immunoglobulin Fc region and the interferon-β protein are fused together by a peptide bond. In another embodiment, the immunoglobulin Fc region and the interferon-β protein are connected by a peptide linker sequence to facilitate protein folding. The linker sequence preferably is composed of glycine and serine residues. For example, in one embodiment, the peptide linker sequence is Gly₄SerGly₄SerGly₃SerGly (SEQ ID NO:1).

In one embodiment, the Fc-interferon-β fusion protein includes amino acid alterations at positions 17, 50, 131, and 140 to improve folding and reduce aggregation. In one specific embodiment, the amino acid alterations are serine substituted in place of cysteine at position 17, histidine substituted in place of phenylalanine at position 50, alanine substituted in place of histidine at position 131, and threonine or alanine substituted in place of histidine at position 140. In certain embodiments, the Fc region includes IgG1, IgG2, or IgG4. The fusion protein can also include a polypeptide linker sequence connecting the interferon-β protein and the immunoglobulin Fc region. In one embodiment, a cysteine residue of the hinge region is mutated.

In another embodiment, the Fc-interferon-β fusion protein includes amino acid alterations at positions 17, 57, 131, and 140, improving folding and reducing aggregation of the expressed fusion protein. In one specific embodiment, the amino acid alterations are serine substituted in place of cysteine at position 17, alanine substituted in place of leucine at position 57, alanine substituted in place of histidine at position 131, and threonine or alanine substituted in place of histidine at position 140. In certain embodiments, the Fc region includes IgG1, IgG2, or IgG4. In another embodiment, the fusion protein can also include a polypeptide linker sequence connecting the interferon-β protein and the immunoglobulin Fc region. In a further embodiment, a cysteine residue of the hinge region is mutated.

The invention also provides methods for encoding and expressing fusion proteins of the invention. For example, one aspect of the invention relates to nucleic acid molecules encoding any of the aforementioned Fc-interferon-β fusion proteins, while in another aspect, the invention relates to cells containing a nucleic acid encoding any of the aforementioned Fc-interferon-β fusion proteins. In a further aspect, the nucleic acid molecules of the invention can be incorporated in operative association into a replicable expression vector which can then be introduced, for example, by transfection, into a mammalian host cell competent to produce the immunoglobulin Fc-IFN-β^(sol) fusion protein. The vector includes a nucleic acid molecule encoding any one of the aforementioned Fc-interferon-β fusion proteins. The invention also encompasses a replicable expression vector for transfecting a mammalian cell. The vector includes a nucleic acid molecule encoding any one of the aforementioned Fc-interferon-β fusion proteins.

In another aspect, the invention relates to methods of stabilizing Fc-interferon-β fusion proteins. In one embodiment, the method includes the step of making any of the aforementioned Fc-interferon-β fusion proteins. In a further embodiment, the stabilizing includes increasing the circulating half-life of the Fc-interferon-β fusion protein relative to an unaltered Fc-interferon-β fusion protein. In yet another embodiment, the stabilizing includes decreasing the aggregation of the Fc-interferon-β fusion protein relative to an unaltered Fc-interferon-β fusion protein, while in a further embodiment, the stabilizing includes increasing the biological activity of the Fc-interferon-β fusion protein relative to an unaltered Fc-interferon-β fusion protein.

A further aspect of the invention relates to methods for treating a patient for a condition alleviated by the administration of interferon-β. In one embodiment, the treatment includes administering an effective amount of any of the aforementioned interferon-β fusion proteins to a mammal having the condition. In another embodiment, the method includes administering a nucleic acid encoding any of the aforementioned interferon-β fusion proteins to a mammal having the condition, while in yet another embodiment, the method includes administering a cell encoding any of the aforementioned interferon-β fusion proteins to a mammal having the condition.

The foregoing and other objects, features and advantages of the invention will be apparent from the description, drawings, and claims that follow.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1C are schematic illustrations of non-limiting examples of Fc-IFN-β^(sol) fusion proteins constructed in accordance with the invention.

FIG. 2 is a photograph of an SDS-PAGE gel showing the migration patterns of HuFc-γ4-IFN-β and HuFc-γ4h-IFN-β fusion proteins without the C17S mutation and HuFc-γ4h-IFN-β(C17S) fusion proteins in both reducing and non-reducing chemical environments.

FIG. 3 is the amino acid sequence for mature IFN-β (SEQ ID NO:2).

FIG. 4 is the amino acid sequence for mature human IFN-β(C17S) (SEQ ID NO:3).

FIG. 5 is the amino acid sequence for human Fc-IFN-β^(sol) (C17S) of theγ4 isotype with a modified γ1 hinge (Fcγ4h-IFN-β^(sol)) (SEQ ID NO:4).

FIG. 6 is the amino acid sequence for human Fc-(linker)-IFN-β, starting with the CH3 domain of the Fcγ4 isotype (SEQ ID NO:5).

FIG. 7 is the amino acid sequence for human Fc-linker)-IFN-β^(sol)(C17S), starting with the CH3 domain of the Fcγ4 isotype (SEQ ID NO:6).

FIG. 8 is the amino acid sequence for human Fc-(linker)-IFN-β^(sol)(C17S L57A H131A H140T) starting with the CH3 domain of the Fcγ4 isotype (SEQ ID NO:7).

FIG. 9 is the amino acid sequence for human Fc-(linker)-IFN-β^(sol)(C17S L57A H131A H140A) starting with the CH3 domain of the Fcγ4 isotype (SEQ ID NO:8).

FIG. 10 is the amino acid sequence for human Fc-(linker)-IFN-β^(sol)(C17S F50A H131A, H140A), starting with the CH3 domain of the Fcγ4 isotype (SEQ ID NO:9).

FIG. 11 is the amino acid sequence for human Fc-(linker)-IFN-β^(sol)(C17S F50A H131A H140T), starting with the CH3 domain of the Fcγ4 isotype (SEQ ID NO:10).

FIG. 12 is the amino acid sequence for mature mouse IFN-β (SEQ ID NO:11).

FIG. 13 is the amino acid sequence for mature mouse IFN-β(C17S) (SEQ ID NO:12).

FIG. 14 is the nucleic acid sequence encoding the fusion protein embodiment huFcγ4h-IFN-β^(sol)(C17S) (γ4 isotype with modified γ1 hinge wherein the first cysteine of the γ1 hinge is replaced by a serine), starting from the hinge region (SEQ ID NO:13).

FIGS. 15-1 through 15-3 show the linearized nucleic acid sequence of the pdCs vector containing huFcγ4h-(linker)-IFN-β^(sol)(C17S) (γ4 isotype with modified γ1 hinge wherein the first cysteine of the γ1 hinge is replaced by a serine), wherein the Fc region and the IFN-β moiety are attached via a linker polypeptide (SEQ ID NO:14).

FIG. 16 is the nucleic acid sequence encoding the fusion protein embodiment HuFc-γ4h-(linker)-IFN-β^(sol)(C17S) (γ4 isotype with modified γ1 hinge wherein the first cysteine of the γ1 hinge is replaced by a serine), starting from the hinge region, wherein the Fc region and the IFN-β moiety are attached via a linker polypeptide (SEQ ID NO:15).

FIGS. 17-1 through 17-3 show the linearized nucleic acid sequence of the pdCs vector containing huFcγ4h-(linker)-IFN-β^(sol)(C17S L57A H131A H140A) (γ4 isotype with modified γ1 hinge wherein the first cysteine of the γ1 hinge is replaced by a serine), wherein the Fe region and the IFN-β moiety are attached via a linker polypeptide (SEQ ID NO:16).

FIG. 18 is the nucleic acid sequence of huFcγ4h-(linker)-IFN-β^(sol)(C17S L57A H131 H140A) (γ4 isotype with modified γ1 hinge wherein the first cysteine of the γ1 hinge is replaced by a serine), starting from the hinge, wherein the Fe region and the IFN-β moiety are attached via a linker polypeptide (SEQ ID NO:17).

FIG. 19-1 through 19-3 shows the linearized nucleic acid sequence of the pdCs vector containing huFcγ4h-(linker)-IFN-β^(sol)(C17S F50H H131A H140A) (γ4 isotype with modified γ1 hinge wherein the first cysteine of the γ1 hinge is replaced by a serine), wherein the Fc region and the IFN-β moiety are attached via a linker polypeptide (SEQ ID NO:18).

FIG. 20 is the nucleic acid sequence of huFcγ4h-(linker)-IFN-β^(sol)(C17S F50H H131A H140A) (γ4 isotype with modified γ1 hinge wherein the first cysteine of the γ1 hinge is replaced by a serine) starting from the hinge, wherein the Fc region and the IFN-β moiety are attached via a linker polypeptide (SEQ ID NO:19).

DETAILED DESCRIPTION OF THE INVENTION

IFN-β mediates antiproliferative, antiviral and immunomodulatory effects and, in addition to its usefulness in treating multiple sclerosis, it is anticipated that many other conditions may be alleviated by IFN-β administration. For example, its usefulness as a treatment for a variety of malignancies, such as acute myeloid leukemia, multiple myeloma, Hodgkin's disease, basal cell carcinoma, cervical dysplasia and osteosarcoma is under evaluation. IFN-β is also being tested as a therapeutic agent against a variety of viral infections, including viral hepatitis, herpes zoster and genitalis, papilloma viruses, viral encephalitis, and cytomegalovirus pneumonia.

However, when administered to a patient, recombinant mature IFN-β has a short circulating half-life, making it suboptimal for use in therapy. Therefore there is a need in the art to produce variants of IFN-β with improved pharmacokinetic properties, including improved serum half-life.

One method known in the art for prolonging the half-life of small proteins involves linking them to an immunoglobulin Fc region. Fusions in which an Fc region is placed at the N-terminus of a ligand (termed ‘immunofusins’ or ‘Fc-X’ fusions, where X is a ligand such as IFN-β) have a number of useful properties (Lo et al., U.S. Pat. Nos. 5,726,044 and 5,541,087; Lo et al. (1998) Protein Engineering 11: 495). For instance, if leptin is administered to a mouse as an Fc-leptin fusion molecule (See, for example, PCT patent application publication WO 00/40615), the circulating half-life of leptin increases from about 18 minutes to more than 8 hours. Similarly, the half-life of IL-2 in a mouse is increased from a few minutes to a few hours when it is administered as an Fc-IL2 fusion protein.

Another useful property of Fc-X fusion proteins is that the Fc portion generally has the effect of increasing protein production significantly. This is believed to occur, in part, because the Fc moiety of the fusion protein, commonly referred to as the expression cassette, is designed for efficient secretion of the fusion protein and, in part, because the fusion proteins can be produced in and secreted from host mammalian cells that naturally express immunoglobulin such that the fusion protein is readily secreted from the host cell. While it may be possible to produce these fusion proteins in a prokaryotic expression system, a eukaryotic expression system is preferred and a mammalian expression system is most preferred.

Surprisingly, it was found that when an unaltered Fc-IFN-β immunofusin was produced in a eukaryotic expression system, it was poorly expressed, misfolded and substantially aggregated. In contrast, recombinant IFN-β proteins produced in a eukaryotic expression system are soluble and 98% monomeric (Runkel et al. (1998), Pharmaceutical Research 15:641). Thus it appeared that the placement of the Fc moiety at the N-terminus of the IFN-β moiety affected the ability of the fusion protein to fold correctly as no aggregation is observed when IFN-β is produced as a fusion protein where the IFN-β moiety precedes the Fc domain (See U.S. Pat. No. 5,908,626). Therefore, there is a need in the art to create Fc-IFN-β fusion proteins that fold correctly and are substantially non-aggregated.

Consequently, the invention provides (i) nucleic acid sequences which facilitate efficient production of immunoglobulin Fc-IFN-β^(sol) fusion proteins; (ii) nucleic acid constructs for rapid and efficient production and secretion of immunoglobulin Fc-IFN-β^(sol) fusion proteins in a variety of mammalian host cells; and (iii) methods for the production, secretion, and purification of recombinant variants of immunoglobulin Fc-IFN-β^(sol) fusion proteins.

In particular, the present invention provides nucleic acid molecules, for example, DNA or RNA molecules, which encode serially in the 5′ to 3′ direction, a polypeptide including an immunoglobulin Fc region and an IFN-β^(sol) protein.

The nucleic acid molecules of the invention can be incorporated in operative association into a replicable expression vector which may then be introduced, for example, by transfection, into a mammalian host cell competent to produce the immunoglobulin Fc-IFN-β^(sol) fusion protein.

The invention also provides methods of stabilizing immunoglobulin Fc-IFN-β fusion proteins. Although many proteins have been successfully produced and purified as Fc fusions, including many four-helix bundle proteins such as IL-2 (huFc-IL2), it has been found that Fc-IFN-β fusion proteins, where IFN-β belongs to the class of four-helix bundle proteins, form aggregates at least partly due to aberrant disulfide bonds present in the protein (“covalent aggregation”). In addition, it has been found that Fc-IFN-β proteins form aggregates through non-covalent interactions as well (“non-covalent aggregation”).

The present invention alleviates aggregation by providing methods of stabilizing Fc-IFN-β fusion proteins including the step of making an Fc-IFN-β^(sol) fusion protein, where the fusion protein includes an IFN-β protein having at one or more amino acid alterations, linked to the carboxy-terminus of an immunoglobulin Fc region. In embodiments of the invention, stabilizing includes increasing the solubility of the Fc-IFN-β^(sol) fusion protein relative to an unaltered Fc-IFN-β fusion protein, increasing the circulating half-life of the Fc-IFN-β^(sol) fusion protein relative to an unaltered Fc-IFN-β fusion protein, and/or enhancing the biological activity of the Fc-IFN-β^(sol) fusion protein relative to an unaltered Fc-IFN-β fusion protein. Increased stabilization is achieved in part by the elimination of aberrant disulfide bonding in the fusion protein and in part by reducing the amount of non-covalent aggregation of the fusion protein.

The invention also provides methods for treating conditions alleviated by IFN-β, bioactive fragments or active variants thereof by administering to a mammal an effective amount of IFN-β produced by a method of the invention and/or an Fc-IFN-β^(sol) fusion protein of the invention. The invention also provides methods for treating conditions alleviated by IFN-β or active variants thereof by administering a nucleic acid of the invention, for example, a “naked DNA,” or a vector containing a DNA or RNA of the invention, to a mammal having the condition.

IFN-β Moiety

The invention provides fusion proteins and nucleic acid molecules encoding those proteins including an altered IFN-β protein linked to the C-terminus of an immunoglobulin Fc region. The IFN-β moiety can include one ore more mutations to the amino acid structure of the IFN-β moiety and Fc-IFN-β construct to improve the protein folding properties of the fusion protein, to reduce aggregation, and to improve protein expression. For example, the IFN-β moiety of the soluble fusion protein Fc-IFN-β^(sol) can contain an alteration at position 17, corresponding to a cysteine in the native mature IFN-β linked to the carboxy-terminus of an immunoglobulin Fc region. The amino acid sequence for native mature human IFN-β is shown in FIG. 3. The amino acid alteration at position 17 of the IFN-β protein can be generated by an amino acid substitution, amino acid deletion or amino acid modification through methods known in the art. Preferred alterations to the IFN-β moiety include substituting either a serine (C17S), valine (C17V), alanine (C17A) or methionine (C17M) in place of the cysteine at position 17. An exemplary amino acid sequence of a soluble human Fc-IFN-β fusion protein containing the C17S mutation (huFc-IFN-β^(sol)(C17S)) is shown in FIG. 5 (SEQ ID NO:4), while the amino acid sequence for an IFN-β moiety including the C17S mutation is shown in FIG. 4 (SEQ ID NO:3). The invention also includes huFc-IFN-β^(sol)(C17V), huFc-IFN-βsol(C17A) and huFc-IFN-β^(sol)(C17M) fusion protein constructs.

In addition to an alteration at position 17 of the mature IFN-β moiety, the invention provides Fc-IFN-β fusion proteins with other altered residues. For example, the IFN-β moiety can be altered at one or more of positions 17, 50, 57, 130, 131, 136, and 140 corresponding to, respectively, a cysteine, a phenylalanine, a lysine, a leucine, a histidine, a lysine, and a histidine in the native mature IFN-β protein. The IFN-β moiety is linked to the carboxy-terminus of an immunoglobulin Fc region. Alterations to the amino acid structure at one or more of positions 17, 50, 57, 130, 131, 136, and 140 can include an amino acid substitution, amino acid deletion or amino acid modification and can be generated through methods known in the art. Alterations introduced at these residues are believed to alleviate the causes of non-covalent aggregation. In one embodiment, the phenylalanine at position 50 is replaced by histidine (F50H). In another embodiment, the leucine at position 57 is replaced by alanine (L57A). In a further embodiment, the histidine at position 131 is replaced by alanine (H131A), while in yet another embodiment, the histidine at 140 is replaced by either alanine (H140A) or threonine (H140T). In another embodiment, the leucine at position 130 is replaced by alanine (L130A), while in yet another embodiment, the lysine at residue 136 is replaced by alanine (K136A). While certain amino acid substitutions have been enumerated herein, the invention is not limited to these enumerated alterations. Any suitable amino acid capable of conferring the appropriate properties on the fusion protein may be substituted in place of the original amino acid residue at position 17, 50, 57, 130, 131, 136, and/or 140 of the IFN-β moiety.

The invention contemplates an IFN-β moiety of an Fc-IFN-β^(sol) fusion protein having any combination of one, two, three, four, five, six, or seven of the alterations to positions 17, 50, 57, 130, 131, 136 and/or 140 as disclosed herein. For example, the Fc-IFN-β^(sol) in one embodiment contains amino acid alterations at one or more of F50, H131 and H140 of the mature form of IFN-β, optionally combined with a C17 alteration. In another embodiment, the IFN-β moiety of the Fc-IFN-β^(sol) fusion protein contains amino acid alterations at one or more of L57, H131 and H140 of the mature form of IFN-β, optionally combined with a C17 alteration. In another embodiment, IFN-β moiety of the Fc-IFN-β^(sol) fusion protein includes the alterations C17S, F50H, H131A, and/or H140A. FIGS. 8-11 show exemplary amino acid sequences of embodiments of Fc-IFN-β^(sol) fusion proteins incorporating various combinations of these mutations. In yet another embodiment, the IFN-β moiety of the Fc-IFN-β^(sol) fusion protein includes the alterations C17S, F50H, H131A, and/or H140T. In yet another embodiment, the IFN-β moiety of the Fc-IFN-β^(sol) fusion protein includes the alterations C17S, L57A, H131A, and/or H140A, while in a further embodiment, the fusion protein includes the alterations C17S, L57A, H131A, and/or H140T. The Fc region is preferably a human Fc region.

Another embodiment of the invention includes nucleic acid sequences encoding Fc-IFN-β^(sol) variants with at least one codon substitution in the mature human IFN-β protein sequence. In one embodiment, a codon substitution replaces the cysteine corresponding to position 17 in the mature human IFN-β sequence with a serine (C17S). Expression of this nucleotide sequence, contained on an appropriate plasmid, in a mammalian cell culture system resulted in the efficient production of the fusion protein huFc-huIFN-β^(sol)(C17S). In alternative embodiments, a codon substitution replaces the cysteine at position 17 with either an alanine, a valine, or a methionine. Similarly, expression from any of these nucleotide sequences, contained on an appropriate plasmid, in a mammalian cell culture system will result in the efficient production of fusion protein huFc-huIFN-β^(sol)(C17A), huFc-huIFN-β^(sol)(C17V), or huFc-huIFN-β^(sol)(C17M). In one embodiment, a nucleic acid sequence encoding a representative Fc-IFN-β^(sol) fusion protein huFcγ4h-IFN-β^(sol)(C17S), starting from the hinge, is disclosed in FIG. 14 (SEQ ID NO:13). The invention also includes nucleic acid sequences encoding Fc-IFN-β^(sol) variants with codon substitutions replacing amino acids at one or more of positions 17, 50, 57, 130, 131, 136 and/or 140. Nucleic acids incorporating the altered codons of the invention can be created using methods known in the art.

The immunoglobulin Fc region and the IFN-β moiety of an Fc-IFN-β^(sol) fusion protein can be linked to one another in a variety of ways. While the C-terminus of the Fc moiety may be directly linked to the N-terminus of the IFN-β moiety via a peptide bond, the invention additionally includes connecting the Fc moiety and the IFN-β moiety via a linker peptide. The linker peptide is located between the C-terminus of the Fc moiety and the N-terminus of the mature IFN-β moiety. The invention also includes a nucleic acid sequence encoding the linker peptide. The linker peptide is preferably composed of serine and glycine residues. In one embodiment, the linker has the amino acid sequence Gly₄SerGly₄SerGly₃SerGly (SEQ ID NO:1), while in yet another embodiment a nucleic acid encoding an Fc-IFN-β^(sol) includes a nucleic acid sequence encoding the linker peptide Gly₄SerGly₄SerGly₃SerGly (SEQ ID NO:1). Some exemplary Fc-linker-IFN-β^(sol) amino acid sequences of the invention are shown in FIGS. 6-11, while some exemplary Fc-linker-IFN-β^(sol) nucleic acid sequences of the invention are shown in FIGS. 14-16. For example, in one embodiment, the Fc-linker-IFN-β^(sol) protein is huFcγ4-linker-IFN-β^(sol)(C17S), wherein the Fc region is an IgG4 Fc region, and the linker is Gly₄SerGly₄SerGly₃SerGly (SEQ ID NO:1). Expression of fusion proteins of the invention from Fc-IFN-β^(sol) and Fc-linker-IFN-β^(sol) nucleotide sequences, such as those previously discussed, when contained on an appropriate plasmid, in a mammalian cell culture system will result in the efficient production of Fc-IFN-β^(sol) and Fc-linker-IFN-β^(sol) fusion proteins.

As previously mentioned, Fc-IFN-β^(sol) fusion proteins of the invention demonstrate improved biological properties over unaltered Fc-IFN-β fusion proteins. For example, it was found that human Fcγ4h-IFN-β^(sol)(C17S) displayed folding properties that were different from, and improved over, the parent fusion protein Fcγ4-IFN-β^(sol) and Fc-γ4h-IFN-β^(sol). In particular, as demonstrated in FIG. 2, it was found that predominantly a single species of the human Fcγ4h-IFN-β^(sol)(C17S) fusion protein 3, 4 was seen when expressed in mammalian tissue culture cells, as ascertained by non-reducing SDS-PAGE gel analysis. This species corresponded to the correctly folded Fcγ4-IFN-β^(sol) fusion protein 3, 4. In contrast, for the parent molecule Fcγ4-IFN-β^(sol) 1 and for Fcγ4h-IFN-β^(sol) 2, many high molecular weight species were observed, as evidenced by an unresolved trail of high molecular weight proteins on a non-reducing SDS-PAGE gel 1, 2. On a reducing SDS-PAGE gel system, this trail resolved to a significant extent into a single band for both human Fcγ4-IFN-β^(sol) 5 and human Fcγ4h-IFN-β^(sol) 6, suggesting that the aggregation was largely driven by the presence of covalent disulfide bonds. Therefore, the introduction of the single point mutation C17S into the human Fcγ4h-IFN-β^(sol) fusion protein 7 restored proper folding of the protein 7.

Moreover, it was found by analytical size exclusion chromatography (SEC), that, whereas non-aggregated protein of the parent molecule could not be obtained, at least 10% of Fc-IFN-β^(sol)(C17S) was non-aggregated after purification with Protein A. Therefore, the introduction of the single point mutation C17S into the Fc-IFN-β^(sol) fusion protein facilitated the production of non-aggregated material. Furthermore, introduction of a linker peptide at the junction between the Fc region and the IFN-β moiety resulted in about a two-fold increase in yield of non-aggregated material over Fc-IFN-β^(sol)(C17S) without the linker. Expression from, for example, a nucleotide sequence encoding the fusion protein Fc-linker-IFN-β^(sol)(C17S F50H H131A H140A) wherein the linker is Gly₄SerGly₄SerGly₃SerGly (SEQ ID NO:1), as shown in FIGS. 19-1 through 19-3, contained on an appropriate plasmid, in a mammalian cell culture system resulted in the efficient production of the fusion protein Fc-linker-IFN-β^(sol)(C17S F50H H131A H140A). It was found that this fusion protein product contained about 50% non-aggregated material after purification by Protein A, as assessed by analytical SEC, which represents a considerable further improvement over the results obtained with Fc-IFN-β^(sol) protein containing a single point mutation in IFN-β, Fc-linker-IFN-β^(sol)(C17S). A similar further increase in expression characteristics was seen with the Fc-IFN-β^(sol) protein Fc-linker-IFN-β^(sol)(C17S L57A H131A H140T).

As previously mentioned, the invention provides nucleic acid sequences encoding and amino acid sequences defining fusion proteins including an immunoglobulin Fc region and at least one target protein, referred to herein as IFN-β or variants thereof. Three exemplary embodiments of protein constructs embodying the invention are illustrated in the drawing as FIGS. 1A-1C. Because dimeric constructs are preferred, all are illustrated as dimers cross-linked by a pair of disulfide bonds between cysteines in adjacent subunits. In the drawings, the disulfide bonds 11, 12 are depicted as linking together the two immunoglobulin heavy chain Fc regions 1, 1′ via an immunoglobulin hinge region within each heavy chain, and thus are characteristic of native forms of these molecules. While constructs including the hinge region of Fc are preferred and have shown promise as therapeutic agents, the invention contemplates that the crosslinking at other positions may be chosen as desired. Furthermore, under some circumstances, dimers or multimers useful in the practice of the invention may be produced by non-covalent association, for example, by hydrophobic interaction. Because homodimeric constructs are important embodiments of the invention, the drawings illustrate such constructs. It should be appreciated, however, that heterodimeric structures also are useful in the practice of the invention.

FIG. 1A illustrates a dimeric construct, also termed a “unit dimer”, produced in accordance with the principles set forth herein (see, for example, Example 1). Each monomer of the homodimer includes an immunoglobulin Fc region I including a hinge region, a CH2 domain and a CH3 domain. Attached directly, i.e., via a polypeptide bond, to the C terminus of the Fc region is IFN-β^(sol) 2. It should be understood that the Fc region may be attached to IFN-β^(sol) protein via a polypeptide linker (not shown).

FIGS. 1B and 1C depict protein constructs of the invention which include as a target protein plural IFN-β proteins arranged in tandem and connected by a linker. In FIG. 1B, the target protein includes full length IFN-β 2, a polypeptide linker made of glycine and serine residues 4, and an active variant of IFN-β 3. This construct may be depicted by the formula Fc-X-X wherein the Xs represent different target proteins. FIG. 1C differs from the construct of FIG. 1B in that the most C-terminal protein domain includes a second, full length copy of IFN-β 2. This construct may be depicted by the formula Fc-X-X, where the Xs represent identical target proteins. Although FIGS. 1A-1C represent Fc-X constructs, where X is the target protein, it is contemplated that useful proteins of the invention may also be depicted by the formula X-Fc-X, wherein the Xs may represent the same or different target proteins.

As shown in FIGS. 1B and 1C, the fusion protein may include a second target protein (Fc-X-X). For example, in addition to a fusion protein having a first IFN-β target protein, the fusion protein may also include a second mature, full length IFN-β or an active IFN-β^(sol) variant or a bioactive fragment thereof. In one aspect, the active variant is a variant in which one or more amino acid residues in the IFN-β moiety is substituted for another amino acid residue. Several IFN-β substitution variants were discussed previously. For example, a cysteine at position 17, corresponding to the native mature IFN-β may be replaced with a serine, a valine, an alanine or a methionine. In this type of construct, the first and second proteins can be the same protein, as in, for example, FIG. 1C, or they may be different proteins, as in, for example, FIG. 1B. The first and second proteins may be linked together, either directly or by means of a polypeptide linker. Alternatively, both proteins may be linked either directly or via a polypeptide linker, to the immunoglobulin Fc region. In a further embodiment, the first protein can be connected to the N-terminus of the immunoglobulin Fc region and the second protein can be connected to the C-terminus of the immunoglobulin Fc region.

In one embodiment, two fusion proteins may be linked to form dimers. The two fusion proteins may associate, either covalently, for example, by a disulfide bond, a polypeptide bond or a crosslinking agent, or non-covalently, to produce a dimeric protein. In a preferred embodiment, the two fusion proteins are associated covalently by means of at least one and more preferably two interchain disulfide bonds via cysteine residues, preferably located within immunoglobulin hinge regions disposed within the immunoglobulin Fc regions of each chain.

Other embodiments of the invention include multivalent and multimeric forms of IFN-β fusion proteins and combinations thereof.

As used herein, the term “multivalent” refers to a recombinant molecule that incorporates two or more biologically active segments. The protein fragments forming the multivalent molecule optionally may be linked through a polypeptide linker which attaches the constituent parts and permits each to function independently.

As used herein, the term “bivalent” refers to a multivalent recombinant molecule having the configuration Fc-X, where X is an IFN-β protein. The two proteins may be linked through a peptide linker. Constructs of the type shown can increase the apparent binding affinity between the protein and its receptor.

As used herein, the term “multimeric” refers to the stable association of two or more polypeptide chains either covalently, for example, by means of a covalent interaction, for example, a disulfide bond, or non-covalently, for example, by hydrophobic interaction. The term multimer is intended to encompass both homomultimers, wherein the subunits are the same, as well as, heteromultimers, wherein the subunits are different.

As used herein, the term “dimeric” refers to a specific multimeric molecule where two polypeptide chains are stably associated through covalent or non-covalent interactions. Such constructions are shown schematically in FIG. 1A. It should be understood that the immunoglobulin Fc region including at least a portion of the hinge region, a CH2 domain and a CH3 domain, typically forms a dimer. Many protein ligands are known to bind to their receptors as a dimer. If a protein ligand X dimerizes naturally, the X moiety in an Fc-X molecule will dimerize to a much greater extent, since the dimerization process is concentration dependent. The physical proximity of the two X moieties connected by Fc would make the dimerization an intramolecular process, greatly shifting the equilibrium in favor of the dimer and enhancing its binding to the receptor.

As used herein, the term “polypeptide linker” is understood to mean a polypeptide sequence that can link together two proteins that in nature are not naturally linked together. The polypeptide linker preferably includes a plurality of amino acids such as alanine, glycine and serine or combinations of such amino acids. Preferably, the polypeptide linker includes a series of glycine and serine peptides about 10-15 residues in length. See, for example, U.S. Pat. Nos. 5,258,698 and 5,908,626. A preferred linker polypeptide of the invention is Gly₄SerGly₄SerGly₃SerGly (SEQ ID NO:1). However, it is contemplated, that the optimal linker length and amino acid composition may be determined by routine experimentation by methods well known in the art.

As used herein, the term “interferon-β or IFN-β” is understood to mean not only full length mature interferon-β, for example, human IFN-β, but also homologs, variants and bioactive fragments or portions thereof. Known sequences of IFN-β may be found in GenBank. The term “interferon-β” or “IFN-β” also includes naturally occurring IFN-β and IFN-β-like proteins, moieties and molecules as well as IFN-β that is recombinantly produced or artificially synthesized.

The term “bioactive fragment” or portion refers to any IFN-β protein fragment that has at least 5%, more preferably at least 10%, and most preferably at least 20% and optimally at least 30%, 40%, 50%, 60%, 70%, 80%, 90% or 100% of the biological activity of the template human IFN-β protein of SEQ ID NO:2, determined using the antiviral activity assay or cellular growth inhibition assays, as described in Examples 6 and 7. The term “variants” includes species and allelic variants, as well as other naturally occurring or non-naturally occurring variants, for example, generated by genetic engineering protocols, that are at least 70% similar or 60% identical, more preferably at least 75% similar or 65% identical, and most preferably at least 80% similar or 70% identical to the mature human IFN-β protein disclosed in SEQ ID NO:2.

In order to determine whether a candidate polypeptide has the requisite percentage similarity or identity to a reference polypeptide, the candidate amino acid sequence and the reference amino acid sequence are first aligned using the dynamic programming algorithm described in Smith and Waterman (1981) J. MOL. BIOL. 147:195-197, in combination with the BLOSUM62 substitution matrix described in FIG. 2 of Henikoff and Henikoff (1992), “Amino acid substitution matrices from protein blocks”, PROC. NATL. ACAD. SCI. USA 89:10915-10919. For the present invention, an appropriate value for the gap insertion penalty is −12, and an appropriate value for the gap extension penalty is −4. Computer programs performing alignments using the algorithm of Smith-Waterman and the BLOSUM62 matrix, such as the GCG program suite (Oxford Molecular Group, Oxford, England), are commercially available and widely used by those skilled in the art.

Once the alignment between the candidate and reference sequence is made, a percent similarity score may be calculated. The individual amino acids of each sequence are compared sequentially according to their similarity to each other. If the value in the BLOSUM62 matrix corresponding to the two aligned amino acids is zero or a negative number, the pair-wise similarity score is zero; otherwise the pair-wise similarity score is 1.0. The raw similarity score is the sum of the pair-wise similarity scores of the aligned amino acids. The raw score then is normalized by dividing it by the number of amino acids in the smaller of the candidate or reference sequences. The normalized raw score is the percent similarity. Alternatively, to calculate a percent identity, the aligned amino acids of each sequence again are compared sequentially. If the amino acids are non-identical, the pair-wise identity score is zero; otherwise the pair-wise identity score is 1.0. The raw identity score is the sum of the identical aligned amino acids. The raw score is then normalized by dividing it by the number of amino acids in the smaller of the candidate or reference sequences. The normalized raw score is the percent identity. Insertions and deletions are ignored for the purposes of calculating percent similarity and identity. Accordingly, gap penalties are not used in this calculation, although they are used in the initial alignment.

Variants may also include other IFN-β mutant proteins having IFN-β-like activity. Species and allelic variants, include, but are not limited to human and mouse IFN-β sequences. The human and mouse mature IFN-β proteins are depicted in SEQ ID NOs.:2 and 11, and in FIGS. 3 and 12 respectively.

Furthermore, the IFN-β sequence may include a portion or all of the consensus sequence set forth in SEQ ID NO:2, wherein the IFN-β has at least 5%, preferably at least 10%, more preferably at least 20%, 30% or 40%, most preferably at least 50%, and optimally 60%, 70%, 80%, 90% or 100% of the biological activity of the mature human IFN-β of SEQ ID NO:2, as determined using the antiviral activity assay or cellular growth inhibition assay of Examples 6 and 7.

The three-dimensional structure of IFN-β has been solved by X-ray crystallography (Karpusas et al, 1997, PNAS 94: 11813). Although in the crystallized state, IFN-β molecule is a dimer with a zinc ion at the dimer interface, it is thought that IFN-β need not be a dimer in order to be active. Structurally IFN-β contains an additional alpha-helical segment with respect to classical four helix bundle proteins, which is formed within the C-D loop, so that the canonical bundle structure is formed by helices A, B, C and E. Interestingly, the structure also reveals a portion of the glycan moiety which is coupled to amino acid N80 at the start of helix C and is ordered along a portion of the protein, most likely shielding some of the surface-exposed hydrophobic amino acid residues from solvent. Glycosylation of IFN-β has been shown to be important for the solubility and stability of the molecule, and this could explain the propensity of the non-glycosylated IFN-β molecule to aggregate. The free cysteine at position 17 in helix A appears proximal to the surface but buried, and, without wishing to be bound by theory, it is possible that scrambled disulfide bonds may in turn prevent the correct glycosylation of the protein.

Dimerization of a ligand can increase the apparent binding affinity between the ligand and its receptor. For instance, if one interferon-beta moiety of an Fc-interferon-beta fusion protein can bind to a receptor on a cell with a certain affinity, the second interferon-beta moiety of the same Fc-Interferon-beta fusion protein may bind to a second receptor on the same cell with a much higher avidity (apparent affinity). This may occur because of the physical proximity of the second interferon-beta moiety to the receptor after the first interferon-beta moiety already is bound. In the case of an antibody binding to an antigen, the apparent affinity may be increased by at least ten thousand-fold, i.e., 104. Each protein subunit, i.e., “X,” has its own independent function so that in a multivalent molecule, the functions of the protein subunits may be additive or synergistic. Thus, fusion of the normally dimeric Fc molecule to interferon-beta may increase the activity of interferon-beta. Accordingly, constructs of the type shown in FIG. 1A may increase the apparent binding affinity between interferon-beta and its receptor.

Fc Moiety

The IFN-β fusion proteins disclosed herein are expressed as fusion proteins with an Fc region of an immunoglobulin. As is known, each immunoglobulin heavy chain constant region includes four or five domains. The domains are named sequentially as follows: CH1-hinge-CH2-CH3(-CH4). The DNA sequences of the heavy chain domains have cross-homology among the immunoglobulin classes, e.g., the CH2 domain of IgG is homologous to the CH2 domain of IgA and IgD, and to the CH3 domain of IgM and IgE.

As used herein, the term, “immunoglobulin Fc region” is understood to mean the carboxyl-terminal portion of an immunoglobulin chain constant region, preferably an immunoglobulin heavy chain constant region, or a portion thereof. For example, an immunoglobulin Fc region may include 1) a CH2 domain 2) a CH3 domain, 3) a CH4 domain 4) a CH2 domain and a CH3 domain, 5) a CH2 domain and a CH4 domain, 6) a CH3 domain and a CH4 domain or 7) a combination of an immunoglobulin hinge region and/or a CH2 domain and/or CH3 domain and/or a CH4 domain. In one embodiment, the immunoglobulin Fc region includes at least an immunoglobulin hinge region, while in another embodiment the immunoglobulin Fc region includes at least one immunoglobulin constant heavy region, for example, a CH2 domain or a CH3 domain, and depending on the type of immunoglobulin used to generate the Fc region, optionally a CH4 domain. In another embodiment, the Fc region includes a hinge region, a CH2 domain and a CH3 domain, and preferably lacks the CH1 domain, while in another embodiment, the Fc region includes a hinge region and a CH2 domain. In yet another embodiment, the Fc region includes a hinge region and a CH3 domain. In a further embodiment, the Fc region contains a functional binding site for the Fc protection receptor, FcRp. The binding site for FcRp includes amino acids in both the CH2 and CH3 domains and the Fc-FcRp interaction contributes significantly to the extended serum half-life of Fc fusion proteins.

Although immunoglobulin Fc regions and component constant heavy domains may be from any immunoglobulin class, a preferred class of immunoglobulin for the Fc-IFN-β fusion proteins of the invention is IgG (Igγ) (γ subclasses 1, 2, 3, or 4). The nucleotide and amino acid sequences of human Fcγ1 are set forth in SEQ ID NOs: 78 and 79. Other classes of immunoglobulin, IgA (Igα), IgD (Igδ), IgE (Igε) and IgM (Igμ), can also be used. The choice of appropriate immunoglobulin heavy chain constant regions is discussed in detail in U.S. Pat. Nos. 5,541,087, and 5,726,044. The choice of particular immunoglobulin heavy chain constant region sequences from certain immunoglobulin classes and subclasses to achieve a particular result is considered to be within the level of skill in the art. The portion of the DNA construct encoding the immunoglobulin Fc region preferably includes at least a portion of a hinge domain, and preferably at least a portion of a CH3 domain of Fcγ or the homologous domains in any of IgA, IgD, IgE, or IgM.

It is contemplated that the Fc region used in the generation of the fusion proteins containing the IFN-β variants can be adapted to the specific application of the molecule. In one embodiment, the Fc region is derived from an immunoglobulin γ1 isotype or variants thereof. The use of human Fcγ1 as the Fc region sequence has several advantages. For example, an Fc region derived from an immunoglobulin γ1 isotype can be used when targeting the fusion protein to the liver is desired. Additionally, if the Fc fusion protein is to be used as a biopharmaceutical, the Fcγ1 domain may confer effector function activities to the fusion protein. The effector function activities include the biological activities such as placental transfer and increased serum half-life. The immunoglobulin Fc region also provides for detection by anti-Fc ELISA and purification through binding to Staphylococcus aureus protein A (“Protein A”). In certain applications, however, it may be desirable to delete specific effector functions from the immunoglobulin Fc region, such as Fc receptor binding and/or complement fixation. When an Fc region derived from immunoglobulin γ1 is used, a lysine at the carboxy terminus of the immunoglobulin Fc region is typically replaced with an alanine. This improves the circulating half life of the Fc-IFN-β^(sol) fusion protein.

Other embodiments of Fc-IFN-β^(sol) fusion proteins use Fc regions derived from a different immunoglobulin γ isotype i.e.γ2, γ3, orγ4, or variants thereof. The Fc region can include a hinge region derived from a different immunoglobulin isotype than the Fc region itself. For example, some embodiments of Fc-IFN-β^(sol) fusion proteins contain a hinge region derived from an immunoglobulin γ1 or a variant thereof. For instance, the immunoglobulin Fc region can be derived from an immunoglobulin γ2 isotype and include a hinge region derived from an immunoglobulin γ1 isotype or a variant thereof. In one embodiment, a cysteine residue of the γ1 hinge is modified. In a further embodiment, the first cysteine of the γ1 hinge is modified. In yet another embodiment, a serine is substituted in place of the first cysteine of the γ1 hinge. Because the immunoglobulin γ2 isotype is ineffective in mediating effector functions and displays vastly reduced binding to Fc↓ receptor (FcγR), it may be expected that this particular configuration of IFN-β fusion variant more closely mimics the biological activity of the free IFN-β molecule and in addition has the most enhanced circulating half-life when administered to a mammal. Just as with γ1, it is preferable to mutate the carboxy-terminal lysine of the Fc region-to alanine in order to improve the circulating half life of the Fc-IFN-β^(sol) fusion protein.

As previously stated, the Fc region of Fc-IFN-β^(sol) fusion proteins of the invention can be derived from an immunoglobulin γ4 isotype. In some embodiments of the invention, an immunoglobulin γ4 isotype is modified to contain a hinge region derived from an immunoglobulin γ1 isotype or a variant thereof. In one embodiment, a cysteine residue of the y1 hinge is modified. In a further embodiment, the first cysteine of the γ1 hinge is modified. In yet another embodiment, a serine is substituted in place of the first cysteine of the γ1 hinge. Like immunoglobulin γ2 isotypes, immunoglobulin γ4 isotypes also exhibit lower affinity towards FcγR and thus offer similar advantages in reducing immune effector functions. When an Fc region derived from γ 1, 2, 3 or 4 is used, a lysine at the carboxy-terminus of the immunoglobulin Fc region is typically replaced with an alanine. Immunoglobulin γ4 is a preferred Fc region for making Fc-IFN-β^(sol) fusion proteins wherein the IFN-β moiety includes alterations to one of more amino acid residues at position 17, 50, 57, 130, 131, 136 and/or 140. An exemplary amino acid sequence of an Fc-IFN-β^(sol) fusion protein of the invention which includes an Fc region of immunoglobulin γ4 isotype modified to contain a hinge region derived from an immunoglobulin γ1 is shown in FIG. 5 (SEQ ID NO:4).

Depending on the application, constant region genes from species other than human, for example, mouse or rat, may be used. The immunoglobulin Fc region used as a fusion partner in the DNA construct generally may be from any mammalian species. Where it is undesirable to elicit an immune response in the host cell or animal against the Fc region, the Fc region may be derived from the same species as the host cell or animal. For example, a human immunoglobulin Fc region can be used when the host animal or cell is human; likewise, a murine immunoglobulin Fc region can be used where the host animal or cell will be a mouse.

Nucleic acid sequences encoding, and amino acid sequences defining a human immunoglobulin Fc region useful in the practice of the invention are set forth in SEQ ID NO:78 and SEQ ID NO:79 respectively. However, it is contemplated that other immunoglobulin Fc region sequences useful in the practice of the invention may be found, for example, by those encoded by nucleotide sequences of the heavy chain constant region which includes the Fc region sequence as disclosed in the Genbank and/or EMBL databases, for example, AF045536.1 (Macaca fuscicularis, nucleotide sequence SEQ ID NO:20; amino acid sequence SEQ ID NO:21), AF045537.1 (Macaca mulatta, nucleotide sequence SEQ ID NO:22; amino acid sequence SEQ ID NO:23), AB016710 (Felis catus, nucleotide sequence SEQ ID NO:24; amino acid sequence SEQ ID NO:25), K00752 (Oryctolagus cuniculus, nucleotide sequence SEQ ID NO:26; amino acid sequence SEQ ID NO:27), U03780 (Sus scrofa, nucleotide sequence SEQ ID NO:28; amino acid sequence SEQ ID NO:29), Z48947 (Camelus dromedaries, nucleotide sequence SEQ ID NO:30), (Bos taurus, nucleotide sequence SEQ ID NO:31; amino acid sequence SEQ ID NO:32), L07789 (Mustela vison, nucleotide sequence SEQ ID NO:33; amino acid sequence SEQ ID NO:34), X69797 (Ovis aries, nucleotide sequence SEQ ID NO:35; amino acid sequence SEQ ID NO:36), U17166 (Cricetulus migratorius, nucleotide sequence SEQ ID NO:37; amino acid sequence SEQ ID NO:38), X07189 (Rattus rattus, nucleotide sequence SEQ ID NO:39; amino acid sequence SEQ ID NO:40), AF157619.1 (Trichosurus vulpecula, nucleotide sequence SEQ ID NO:41; amino acid sequence SEQ ID NO:42), or AF035195 (Monodelphis domestica, nucleotide sequence SEQ ID NO:43; amino acid sequence SEQ ID NO:44).

Furthermore, it is contemplated that substitution or deletion of amino acids within the immunoglobulin heavy chain constant regions may be useful in the practice of the invention. One example may include introducing amino acid substitutions in the upper CH2 region to create an Fc variant with reduced affinity for Fc receptors (Cole et al. (1997) J. Immunol. 159:3613). One of ordinary skill in the art can prepare such constructs using well known molecular biology techniques.

It is understood that the present invention exploits conventional recombinant DNA methodologies for generating the Fc fusion proteins useful in the practice of the invention. The Fc fusion constructs preferably are generated at the DNA level, and the resulting DNAs integrated into expression vectors, and expressed to produce the fusion proteins of the invention.

As used herein, the term “vector” is understood to mean any nucleic acid including a nucleotide sequence competent to be incorporated into a host cell and to be recombined with and integrated into the host cell genome, or to replicate autonomously as an episome. Such vectors include linear nucleic acids, plasmids, phagemids, cosmids, RNA vectors, viral vectors and the like. Non-limiting examples of a viral vector include a retrovirus, an adenovirus and an adeno-associated virus. As used herein, the term “gene expression” or “expression” of a target protein, is understood to mean the transcription of a DNA sequence, translation of the mRNA transcript, and secretion of an Fc fusion protein product.

A useful expression vector is pdCs (Lo et al. (1988) Protein Engineering 11:495), in which the transcription of the Fc-X gene utilizes the enhancer/promoter of the human cytomegalovirus and the SV40 polyadenylation signal. The enhancer and promoter sequence of the human cytomegalovirus used was derived from nucleotides −601 to +7 of the sequence provided in Boshart et al. (1985) Cell 41:521. The vector also contains the mutant dihydrofolate reductase gene as a selection marker (Simonsen and Levinson (1983) Proc. Nat. Acad. Sci. USA 80:2495).

An appropriate host cell can be transformed or transfected with the DNA sequence of the invention, and utilized for the expression and/or secretion of the target protein. Currently preferred host cells for use in the invention include immortal hybridoma cells, NS/0 myeloma cells, 293 cells, Chinese hamster ovary cells, HeLa cells, and COS cells.

One expression system that has been used to produce high level expression of fusion proteins in mammalian cells is a DNA construct encoding, in the 5′ to 3′ direction, a secretion cassette, including a signal sequence and an immunoglobulin Fc region, and a target protein such as IFNβ. Several target proteins have been expressed successfully in such a system and include, for example, IL2, CD26, Tat, Rev, OSF-2, βIG-H3, IgE Receptor, PSMA, and gp120. These expression constructs are disclosed in U.S. Pat. Nos. 5,541,087 and 5,726,044 to Lo et al.

The fusion proteins of the invention may or may not be include a signal sequence when expressed. As used herein, the term “signal sequence” is understood to mean a segment which directs the secretion of the IFN-β fusion protein and thereafter is cleaved following translation in the host cell. The signal sequence of the invention is a polynucleotide which encodes an amino acid sequence which initiates transport of a protein across the membrane of the endoplasmic reticulum. Signal sequences which are useful in the invention include antibody light chain signal sequences, e.g., antibody 14.18 (Gillies et. al. (1989) J. Immunol. Meth. 125:191), antibody heavy chain signal sequences, e.g., the MOPC141 antibody heavy chain signal sequence (Sakano et al. (1980) Nature 286:5774), and any other signal sequences which are known in the art (see, e.g., Watson (1984) Nucleic Acids Research 12:5145).

Signal sequences have been well characterized in the art and are known typically to contain 16 to 30 amino acid residues, and may contain greater or fewer amino acid residues. A typical signal peptide consists of three regions: a basic N-terminal region, a central hydrophobic region, and a more polar C-terminal region. The central hydrophobic region contains 4 to 12 hydrophobic residues that anchor the signal peptide across the membrane lipid bilayer during transport of the nascent polypeptide. Following initiation, the signal peptide is usually cleaved within the lumen of the endoplasmic reticulum by cellular enzymes known as signal peptidases. Potential cleavage sites of the signal peptide generally follow the “(−3, −1) rule.” Thus a typical signal peptide has small, neutral amino acid residues in positions −1 and −3 and lacks proline residues in this region. The signal peptidase will cleave such a signal peptide between the −1 and +1 amino acids. Thus, the signal sequence may be cleaved from the amino-terminus of the fusion protein during secretion. This results in the secretion of an Fc fusion protein consisting of the immunoglobulin Fc region and the target protein. A detailed discussion of signal peptide sequences is provided by von Heijne (1986) Nucleic Acids Res. 14:4683.

As would be apparent to one of skill in the art, the suitability of a particular signal sequence for use in the secretion cassette may require some routine experimentation. Such experimentation will include determining the ability of the signal sequence to direct the secretion of an Fc fusion protein and also a determination of the optimal configuration, genomic or cDNA, of the sequence to be used in order to achieve efficient secretion of Fc fusion proteins. Additionally, one skilled in the art is capable of creating a synthetic signal peptide following the rules presented by von Heijne, referenced above, and testing for the efficacy of such a synthetic signal sequence by routine experimentation. A signal sequence can also be referred to as a “signal peptide,” “leader sequence,” or “leader peptides.”

The fusion of the signal sequence and the immunoglobulin Fc region is sometimes referred to herein as secretion cassette. An exemplary secretion cassette useful in the practice of the invention is a polynucleotide encoding, in a 5′ to 3′ direction, a signal sequence of an immunoglobulin light chain gene and an Fcγ1 region of the human immunoglobulin γ1 gene. The Fcγ1 region of the immunoglobulin Fcγ1 gene preferably includes at least a portion of the immunoglobulin hinge domain and at least the CH3 domain, or more preferably at least a portion of the hinge domain, the CH2 domain and the CH3 domain. As used herein, the “portion” of the immunoglobulin hinge region is understood to mean a portion of the immunoglobulin hinge that contains at least one, preferably two cysteine residues capable of forming interchain disulfide bonds. The DNA encoding the secretion cassette can be in its genomic configuration or its cDNA configuration. Under certain circumstances, it may be advantageous to produce the Fc region from human immunoglobulin Fcγ2 heavy chain sequences. Although Fc fusions based on human immunoglobulin γ1 andγ2 sequences behave similarly in mice, the Fc fusions based on the γ2 sequences can display superior pharmacokinetics in humans.

In another embodiment, the DNA sequence encodes a proteolytic cleavage site interposed between the secretion cassette and the target protein. A cleavage site provides for the proteolytic cleavage of the encoded fusion protein thus separating the Fc domain from the target protein. As used herein, “proteolytic cleavage site” is understood to mean amino acid sequences which are preferentially cleaved by a proteolytic enzyme or other proteolytic cleavage agents. Useful proteolytic cleavage sites include amino acids sequences which are recognized by proteolytic enzymes such as trypsin, plasmin or enterokinase K. Many cleavage site/cleavage agent pairs are known (see, for example, U.S. Pat. No. 5,726,044).

Further, substitution or deletion of constructs of these constant regions, in which one or more amino acid residues of the constant region domains are substituted or deleted also would be useful. One example would be to introduce amino acid substitutions in the upper CH2 region to create an Fc variant with reduced affinity for Fc receptors (Cole et al. (1997) J. Immunol. 159: 3613). One of ordinary skill in the art can prepare such constructs using well known molecular biology techniques.

The fusion constructs disclosed herein produced high levels of Fc-IFN-β^(sol). The initial clones produced about 100 μg/mL of altered Fc-IFN-β^(sol), which could be purified to homogeneity by Protein A affinity chromatography. Expression levels often can be increased several fold by subcloning. As stated above, it was found that when IFN-β with the cysteine at position 17 replaced with a serine, an alanine, a valine or a methionine is expressed as Fc fusion molecules, high levels of expression were obtained, presumably because the amino acid substitution at position 17 of the IFN-β^(sol) protein prevents aberrant disulfide bond formation in the protein and the Fc region acts as a carrier, helping the polypeptide to fold correctly and to be secreted efficiently. Similarly, other Fc-IFN-β^(sol) fusion proteins of the invention including the mutation C17S, such as, for example Fc-(linker)-IFN-β^(sol)(C17S F50H H131A -H140A) and Fc-(linker)-IFN-β^(sol)(C17S L57A H131A H140T) are equally well expressed. Moreover, the Fc region is also glycosylated and highly charged at physiological pH. Therefore, the Fc region can help to solubilize hydrophobic proteins.

In addition to high levels of expression, Fc-IFN-β^(sol) proteins exhibited greater bioactivity than the parental (un-modified) Fc-IFN-β fusion protein, as measured in a cell based anti-viral assay (Example 6), and were comparable to the bioactivity of a commercial preparation of IFN-β obtained from R&D Systems (Minneapolis, Minn.).

In addition to the high levels of expression, altered Fc-IFN-β fusion proteins exhibited longer serum half-lives compared to unaltered Fc-IFN-β fusion proteins. For example, the circulating half-life of Fc-IFN-β^(sol) including the mutation C17S is found to be significantly greater than that of the parent Fc-IFN-β fusion protein (see Example 8).

The fusion proteins of the invention provide several important clinical benefits. As demonstrated in the tests of biological assays in Examples 6 and 7, the biological activity of altered Fc-IFN-β^(sol) is significantly higher than that of unaltered Fc-IFN-β.

Another embodiment of the present invention provides constructs having various structural conformations, e.g., bivalent or multivalent constructs, dimeric or multimeric constructs, and combinations thereof. Such functional conformations of molecules of the invention allow the synergistic effect of IFN-β and other anti-viral and anti-cancer proteins to be explored in animal models.

An important aspect of the invention is that the sequences and properties of various IFN-β proteins and encoding DNAs are quite similar. In the context of Fc-X fusions, the properties of IFN-β proteins and encoding DNAs are essentially identical, so that a common set of techniques can be used to generate any Fc-IFN-β DNA fusion, to express the fusion, to purify the fusion protein, and to administer the fusion protein for therapeutic purposes.

The present invention also provides methods for the production of IFN-β of non-human species as Fc fusion proteins. Non-human IFN-β fusion proteins are useful for preclinical studies of IFN-β because efficacy and toxicity studies of a protein drug must be performed in animal model systems before testing in human beings. A human protein may not work in a mouse model since the protein may elicit an immune response, and/or exhibit different pharmacokinetics skewing the test results. Therefore, the equivalent mouse protein is the best surrogate for the human protein for testing in a mouse model.

The present invention provides methods of treating various cancers, viral diseases, other diseases, related conditions and causes thereof by administering the DNA, RNA or proteins of the invention to a mammal having such condition. Related conditions may include, but are not limited to multiple sclerosis; a variety of malignancies, such as acute myeloid leukemia, multiple myeloma, Hodgkin's disease, basal cell carcinoma, cervical dysplasia and osteosarcoma; a variety of viral infections, including viral hepatitis, herpes zoster and genitalis, papilloma viruses, viral encephalitis, and cytomegalovirus pneumonia.

In view of the broad roles played by IFN-β in modulating immune responses, the present invention also provides methods for treating conditions alleviated by the administration of IFN-β. These methods include administering to a mammal having the condition, which may or may not be directly related to viral infection or cancer, an effective amount of a composition of the invention. For example, a nucleic acid, such as DNA or RNA, encoding an Fc-IFN-β^(sol) fusion protein can be administered to a subject, preferably a mammal, as a therapeutic agent. Additionally, a cell containing a nucleic acid encoding an Fc-IFN-β^(sol) fusion protein can be administered to a subject, preferably a mammal, as a therapeutic agent. Furthermore, an Fc-IFN-β^(sol) protein can be administered to a subject, preferably a mammal, as a therapeutic agent.

The proteins of the invention not only are useful as therapeutic agents, but one skilled in the art recognizes that the proteins are useful in the production of antibodies for diagnostic use. Likewise, appropriate administration of the DNA or RNA, e.g., in a vector or other delivery system for such uses, is included in methods of use of the invention.

Compositions of the present invention may be administered by any route which is compatible with the particular molecules. It is contemplated that the compositions of the present invention may be provided to an animal by any suitable means, directly (e.g., locally, as by injection, implantation or topical administration to a tissue locus) or systemically (e.g., parenterally or orally). Where the composition is to be provided parenterally, such as by intravenous, subcutaneous, ophthalmic, intraperitoneal, intramuscular, buccal, rectal, vaginal, intraorbital, intracerebral, intracranial, intraspinal, intraventricular, intrathecal, intracisternal, intracapsular, intranasal or by aerosol administration, the composition preferably includes part of an aqueous or physiologically compatible fluid suspension or solution. Thus, the carrier or vehicle is physiologically acceptable so that in addition to delivery of the desired composition to the patient, it does not otherwise adversely affect the patient's electrolyte and/or volume balance. The fluid medium for the agent thus can include normal physiologic saline.

The DNA constructs (or gene constructs) of the invention also can be used as a part of a gene therapy protocol to deliver nucleic acids encoding IFN-β or a fusion protein construct thereof. The invention features expression vectors for in vivo transfection and expression of IFN-β or a fusion protein construct thereof in particular cell types so as to reconstitute or supplement the function of IFN-β. Expression constructs of IFN-β, or fusion protein constructs thereof, may be administered in any biologically effective carrier, e.g. any formulation or composition capable of effectively delivering the IFN-β gene or fusion protein construct thereof to cells in vivo. Approaches include insertion of the subject gene in viral vectors including recombinant retroviruses, adenovirus, adeno-associated virus, and herpes simplex virus-1, or recombinant bacterial or eukaryotic plasmids. Preferred dosages per administration of nucleic acids encoding the fusion proteins of the invention are within the range of 1 μg/m2 to 100 mg/m2, more preferably 20 μg/m2 to 10 mg/m2, and most preferably 400 μg/m2 to 4 mg/m2. It is contemplated that the optimal dosage and mode of administration may be determined by routine experimentation well within the level of skill in the art.

Preferred dosages of the fusion protein per administration are within the range of 0.1 mg/m2-100 mg/m2, more preferably, 1 mg/m2-20 mg/m2, and most preferably 2 mg/m2-6 mg/m2. It is contemplated that the optimal dosage, however, also depends upon the disease being treated and upon the existence of side effects. However, optimal dosages may be determined using routine experimentation. Administration of the fusion protein may be by periodic bolus injections, or by continuous intravenous or intraperitoneal administration from an external reservoir (for example, from an intravenous bag) or internal (for example, from a bioerodable implant). Furthermore, it is contemplated that the fusion proteins of the invention also may be administered to the intended recipient together with a plurality of different biologically active molecules. It is contemplated, however, that the optimal combination of fusion protein and other molecules, modes of administration, dosages may be determined by routine experimentation well within the level of skill in the art.

The invention is illustrated further by the following non-limiting examples.

EXAMPLES Example 1 Cloning of huFc-huInterferon-beta (huFc-IFN-β) and huFc-IFN-β^(sol) Mutants

Human interferon β (IFN-β) cDNA was ordered from American Type Culture Collection (ATCC Number 31903). The sequence for the mature form was amplified by Polymerase Chain Reactions (PCR). The forward primer used in the amplification reactions was 5′ C CCG GGT ATG AGC TAC AAC TTG CTT (SEQ ID NO:45), where the sequence CCCGGGT encodes the carboxy terminus of the CH3 without the lysine codon, as well as the restriction endonuclease site SmaI CCCGGG (Lo et al., Protein Engineering (1998) 11:495), and the sequence in bold encodes the N-terminus of the mature IFN-β coding sequence. The reverse primer for this reaction was 5′ CTC GAG TCA GTT TCG GAG GTA ACC TGT (SEQ ID NO:46), where TCA is the anticodon of the translation stop codon, and CTCGAG is the restriction site Xho I. The amplified 450 bp PCR product was cloned into the pCRII vector (Invitrogen), and its sequence verified.

The SmaI-XhoI restriction fragment with the completely correct mature IFN-β sequence was used for cloning into the expression vector pdCs-huFc, such that the coding sequence of mature IFN-β was fused in frame to the 3′-end of the Fc coding sequence. The expression plasmid pdCs-huFc-IFN-β was constructed by ligating the SmaI-XhoI restriction fragment containing the mature IFN-β cDNA with the SmaI-XhoI restriction fragment of the pdCs-huFc vector according to Lo et al., (Protein Engineering (1998) 11:495). The huFc DNA corresponds to a sequence that when expressed produces the Fc fragment of the human immunoglobulin γ4 with a modified γ1 hinge sequence. The amino acid sequence is shown in SEQ ID NO:77.

To generate further fusion proteins including the IFN-β fused to Fc moieties of a different isotype or containing other alterations, the same cloning strategy was used, while substituting the appropriate version of pdCs-huFc vector. Thus, the SmaI-XhoI restriction fragment of IFN-β was inserted into pdCS-huFc vector digested with SmaI and XhoI, which encoded either an immunoglobulin γ 4 isotype with a γ 4-derived hinge region, or an immunoglobulin γ 1 isotype, or an immunoglobulin γ 2 isotype, or an immunoglobulin γ2 isotype but with an altered immunoglobulin γ 1-derived hinge region. Because the introduction of the SmaI cloning site into the vector encoding an immunoglobulin γ 4 isotype does not result in a silent mutation in the expressed protein of the Fc moiety, the protein sequence encoded by the nucleic acid sequence around the SmaI site is LSLSPG (SEQ ID NO:53). Had the mutation been silent, the sequence would have present been LSLSLG (See e.g. FIG. 7, residues 101-106 or SEQ ID NO:76).

The cysteine 17 to serine (C17S) mutation was introduced into the IFN-β nucleotide sequence by an overlapping PCR method (Daugherty et al., (1991) Nucleic Acids Res. 19:2471) using complementary mutagenic primers. The forward primer sequence was: 5′ AGA AGC AGC AAT TTT CAG AGT CAG AAG CTC CTG TGG CA (SEQ ID NO:47), where the underlined nucleotide indicates the introduced point mutation (TGT to AGT). Accordingly, the reverse primer was: 5′ TG CCA CAG GAG CTT CTG ACT CTG AAA ATT GCT GCT TCT (SEQ ID NO:48). The PCR fragment generated by the overlapping PCR method was ligated to the pCRII vector, the sequence verified, and the SmaI-XhoI fragment ligated to any of the pdCs-huFc expression vectors as described above. The amino acid sequence is shown as SEQ ID NO:3. The sequence of the mouse counterpart with the mutation is depicted in SEQ ID NO:12.

As discussed above, the cysteine at position 17 is mutated to a serine in the Fc-IFN-β^(sol) protein that has the Fc portion including immunoglobulin γ 4 with a modified γ 1 hinge sequence. The amino acid sequence is shown as SEQ ID NO:4.

To introduce a flexible linker sequence between the huFc moiety and the IFN-β moiety, a synthetic oligonucleotide duplex of the sequence 5′ G GGT GCA GGG GGC GGG GGC AGC GGG GGC GGA GGA TCC GGC GGG GGC TC 3′ (SEQ ID NO:49) was produced. This blunt-ended, double-stranded duplex was inserted at the unique SmaI site of the expression vector pdCs-huFc-IFN-β by ligation. The orientation of the blunt-ended duplex in the resultant vector, pdCs-huFc-(GS linker)-IFN-β was confirmed by sequencing. As a result, the amino acid sequence GAGGGGSGGGGSGGGS (SEQ ID NO:50) was added between the proline (codon CCG) and the glycine (codon GGT) residues encoded by the C CCG GGT (SEQ ID NO:51) sequence containing the SmaI site. The amino acid sequence of a huFc-(GS linker) IFN-β starting with the CH3 domain of the Fcγ4 isotype is shown in FIG. 6 (SEQ ID NO:5). When using this linker with immunoglobulin γ4 constructs of the invention, it is important to note that LSLSPG (SEQ ID NO:52) C-terminal amino acid sequence of immunoglobulin γ4 lacks the alanine residue present in the immunoglobulin γ1, γ2 or γ3 C-terminal sequence LSLSPGA (SEQ ID NO:53). As stated earlier, the alanine is the result of mutating the native lysine residue. When the linker is inserted in the γ1, γ2 orγ3 construct, terminal glycine and alanine residues are identically substituted by a glycine and alanine of the linker. Thus, when the linker is inserted into immunoglobulin γ4 Fc-IFN-β, the amino acid sequence gains an additional alanine residue when the C-terminal glycine is replaced by glycine and alanine. This is exemplified by comparing, for example, FIG. 5, residues 226-231 (SEQ ID NO:4) and FIG. 6, beginning at residue 101 (SEQ ID NO:5).

Further Fc-IFN-β^(sol) protein variants can be produced that contain mutations in the IFN-β moiety. For example, C17 may be altered to another amino acid, for instance alanine. In order to introduce the C17A mutation, the following mutagenic oligonucleotides are used: the forward primer is 5′ AGA AGC AGC AAT TTT CAG GCT CAG AAG CTC CTG TGG CA 3′, (SEQ ID NO:54), and the reverse primer is 5′ TG CCA CAG GAG CTT CTG AGC CTG AAA ATT GCT GCT TCT 3′, (SEQ ID NO:55), where the underlined nucleotides indicate the introduced mutations.

Further mutations in Fc-IFN-β^(sol) were introduced in the IFN-β moiety by overlap PCR. Preferred IFN-β fusion proteins of the invention, Fcγ4h-(linker)-IFN-β^(sol)(C17S L57A H131A H140A) and Fcγ4h-(linker)-IFN-β^(sol)(C17S F50H H131A H140A), are produced by starting with the template Fcγ4h-linker-IFN-βsol(C17S) prepared using methods previously described herein.

To introduce the H131A mutation to the Fcγ4h-(linker)-IFN-β^(sol)(C 17S) template, a first nucleic acid fragment is created by PCR using the forward primer sequence 5′ CTC CCT GTC CCC GGG TGC AGG GGG (SEQ ID NO:56), which incorporates the restriction endonuclease XmaI site, and the reverse primer sequence 5′ CTT GGC CTT CAG GTA GGC CAG AAT CCT CCC ATA ATA TC (SEQ ID NO:57), where GGC represents the H131A mutation. A second fragment of the fusion protein is created by PCR using the forward primer sequence 5′GAT ATT ATG GGA GGA TTC TGG CCT ACC TGA AGG CCA AG (SEQ ID NO:58), where GGC represents the H131A mutation, and the reverse primer sequence 5′ CTT ATC ATG TCT GGA TCC CTC GAG (SEQ ID NO:59), which incorporates the BamHI restriction site. The products from these reactions are purified on an electrophoretic gel according to standard methods. The gel purified fragments are then together subjected to PCR using the forward primer sequence 5′CTC CCT GTC CCC GGG TGC AGG GGG (SEQ ID NO:60), which incorporates the XmaI restriction site, and the reverse primer sequence 5′ CTT ATC ATG TCT GGA TCC CTC GAG (SEQ ID NO:61), which incorporates the BamHI restriction site. This results in a nucleic acid encoding Fcγ4h-linker-IFN-βsol(C17S H131A).

Next, the H140A mutation is introduced by subjecting the Fcγh-linker-IFN-β^(sol)(C17S H131A) to PCR to create a first fragment using the forward primer sequence 5′CTC CCT GTC CCC GGG TGC AGG GGG (SEQ ID NO:62), which incorporates the restriction endonuclease XmaI site, and the reverse primer sequence 5′ GGT CCA GGC ACA GGC ACT GTA CTC CTT GGC (SEQ ID NO:63), where GGC represents the H140A mutation. A second fragment of the fusion protein is created by PCR using the forward primer sequence 5′ GGC AAG GAG TAC AGT GCC TGT GCC TGG ACC (SEQ ID NO:64), where GCC represents the H140A mutation. The reverse primer sequence is 5′ CTT ATC ATG TCT GGA TCC CTC GAG (SEQ ID NO:65), which incorporates the BamHI restriction site. The products from these reactions are purified on an electrophoretic gel according to standard methods. The gel purified fragments are then together subjected to PCR using the forward primer sequence 5′CTC CCT GTC CCC GGG TGC AGG GGG (SEQ ID NO:66), which incorporates the XmaI restriction site, and the reverse primer sequence 5′ CTT ATC ATG TCT GGA TCC CTC GAG (SEQ ID NO:67), which incorporates the BamHI restriction site. This results in a nucleic acid encoding Fcγ4h-linker-IFN-β^(sol)(C17S H131A H140A). Alternatively, this process may be followed to instead insert the H140T mutation of the invention by modifying the appropriate primers to express the threonine codon ACC.

Finally, to introduce either the F50H mutation or the L57A mutation to the template Fcγ4h-linker-IFN-β^(sol)(C17S H131A H140A) template prepared in the previous step, a first nucleic acid fragment is created by PCR using the forward primer 5′CTC CCT GTC CCC GGG TGC AGG GGG (SEQ ID NO:68), which incorporates the restriction endonuclease XmaI site, and either the reverse primer sequence 5′ GAG CAT CTC ATA GAT GGT GGC TGC GGC GTC CT C (SEQ ID NO:69), where GGC represents the codon for creating the L57A mutation or the reverse primer sequence 5′ GTC CTC CTT CTG ATG CTG CTG CAG CTG (SEQ ID NO:70), where ATG represents the codon creating the F50H mutation. To create the second fragment of the fusion protein for the L57A mutation, the template is subjected to PCR using the forward primer sequence 5′ GAG GAC GCC GCA GCC ACC ATC TAT GAG ATG CTC (SEQ ID NO:71), where GCC represents the L57A mutation. To create the second fragment of the fusion protein for introducing the F50H mutation, the template is subjected to PCR using the forward primer sequence 5′ CAG CTG CAG CAG CAT CAG AAG GAG GAC (SEQ ID NO:72), where CAT represents the F50H mutation. The reverse primer for production of the second fragment of either mutation is 5′ CTT ATC ATG TCT GGA TCC CTC GAG (SEQ ID NO:73), which incorporates the BamHI restriction site. The products from these reactions are purified on an electrophoretic gel according to standard methods. The gel purified fragments are then used as the PCR to produce a nucleic acid encoding Fcγ4h-linker-IFN-β^(sol)(C17S L57A H131A H140A) or Fcγ4h-linker-IFN-β^(sol)(C17S F50H H131A H140A). The forward and reverse primers for this reaction are 5′CTC CCT GTC CCC GGG TGC AGG GGG (SEQ ID NO:74) and 5′ CTT ATC ATG TCT GGA TCC CTC GAG (SEQ ID NO:75), respectively, as used in previous steps.

Example 2 Transfection and Expression of Fc-IFN-β Fusion Proteins

For rapid analysis of protein expression, the plasmid pdCs-huFc-IFN-β, pdCs-huFc-IFN-β^(sol)(C17S) or other huFc fusion protein variants containing huIFN-β were introduced into human embryonic kidney HEK 293 cells (ATCC# CRL-1573) by transient transfection using lipofectamine (Invitrogen).

To obtain stably transfected clones which express huFc-IFN-β^(sol)(C17S), for example, the appropriate plasmid DNA was introduced into the mouse myeloma NS/0 cells by electroporation. NS/0 cells were grown in Dulbecco's modified Eagle's medium supplemented with 10% heat-inactivated fetal bovine serum, 2 mM glutamine and penicillin/streptomycin. About 5×10⁶ cells were washed once with PBS and resuspended in 0.5 ml PBS. 10 μg of linearized plasmid DNA were then incubated with the cells in a Gene Pulser Cuvette (0.4 cm electrode gap, BioRad) on ice for 10 min. Electroporation was performed using a Gene Pulser (BioRad, Hercules, Calif.) with settings at 0.25 V and 500 μF. Cells were allowed to recover for 10 min on ice, after which they were resuspended in growth medium and plated onto two 96 well plates. Stably transfected clones were selected by their growth in the presence of 100 nM methotrexate (MTX), which was added to the growth medium two days post-transfection. The cells were fed every 3 days for two to three more times, and MTX-resistant clones appeared in 2 to 3 weeks. Supernatants from clones were assayed by anti-Fc ELISA to identify high producers. High producing clones were isolated and propagated in growth medium containing 100 nM MTX. The growth medium typically used was H-SFM or CD medium (Life Technologies).

Alternatively, clones stably expressing huFc-IFN-β^(sol) fusion proteins were obtained in human embryonic kidney HEK 293 cells by methotrexate selection, by a method similar to the one described above. HEK 293 clones were maintained in DMEM supplemented with 10% FBS.

Example 3 Characterization of huFc-IFN-β Fusion Proteins from Cell Supernatants

The huFc-IFN-β fusion proteins were subsequently captured from the medium for further analysis. For routine characterization by gel electrophoresis, the huFc-IFN-β fusion proteins secreted into the medium was captured on Protein A Sepharose beads (Repligen, Cambridge, Mass.) and then eluted by boiling the sample in protein sample buffer, with or without a reducing agent such as β-mercaptoethanol. The samples were analyzed by SDS-PAGE and the protein bands were visualized by Coomassie staining.

When huFc-IFN-β protein containing an immunoglobulin γ 4 isotype was analyzed by SDS-PAGE, it was found that the protein was not expressed in mammalian tissue culture cells as a uniform species. As shown in FIG. 2, under non-reducing conditions, in addition to a major band at 100 kDa which represented the huFc-IFN-β, multiple other bands were clearly visible, as well as an unresolved trail of higher molecular weight proteins. These results indicated that when expressed as an Fc fusion protein, the wildtype IFN-β formed aggregates. This finding was in contrast to what is generally found with unmodified IFN-β; when the wildtype sequence is cloned into an expression vector, and expressed and secreted in mammalian cell culture it is found to be 98% monomeric by size exclusion chromatography (Runkel et al., (1998), Pharmaceutical Research 15:641). This result was further unexpected in light of the fact that IFN-β can be produced as a fusion protein of the form IFN-β-Fc. See, for example, U.S. Pat. No. 5,908,626.

A portion of these aggregates was stable to reducing agents, as additional bands to the expected 50 kDa band for huFc-IFN-β persisted in a reducing SDS-PAGE system. However, the amount of material exhibiting abnormal migration was vastly diminished. This result suggested that to a significant extent the aggregation was due to scrambled disulfide bond formation.

An Fc-IFN-β variant which contained a substitution of the hinge region with one derived from immunoglobulin γ 1 was analyzed. It was found that this substitution had no impact on the behavior of the fusion protein, although it did not contain four disulfide bonds like the immunoglobulin γ 4 hinge region. Similarly, using an Fc isotype derived from an immunoglobulin γ 1 in the fusion construct also had no effect. Thus, while the aggregation appeared to be due to the presence of the Fc moiety, the aggregation could not be alleviated by alterations in the Fc moiety.

It has been reported that when IFN-β is fused to the N-terminal region of Fc, the introduction of a linker sequence is useful. See, for example, U.S. Pat. No. 5,908,626. Similar to the Fc-IFN-β fusion proteins with either the altered hinge regions or altered Fc regions, an Fc-IFN-β fusion protein containing a Gly-Ser linker region, which separates the Fc region from the IFN-β moiety also yields the same result as above.

In contrast, SDS-PAGE analysis of huFc-IFN-β(C17S) revealed that this protein was substantially non-aggregated. Under non-reducing conditions, the band of 100 kDa corresponding to huFc-IFN-β (C17S) represented practically the only visible band on the gel. Moreover, under reducing conditions, the more prominent band representing aggregated fusion protein, most probably due to interaction of exposed hydrophobic patches, was also absent. Therefore, the introduction of a cysteine substitution at position 17 of the mature sequence of IFN-β promoted the correct folding of the fusion protein. This result was surprising on two counts: for one, the presence of a free cysteine in the “X” portion of an Fc-X protein had not presented a problem in other fusion proteins, such as Fc-IL2; and the presence of the free cysteine in IFN-β had not presented a problem either when the free protein or when an IFN-β-Fc protein were expressed in a mammalian expression system.

Example 4 ELISA Procedures

The concentration of human Fc-containing protein products in the supernatants of MTX-resistant clones and other test samples were determined by anti-huFc ELISA. Standard procedures as described in detail below were essentially followed.

A. Coating Plates

ELISA plates were coated with AffiniPure Goat anti-Human IgG (H+L) (Jackson Immuno Research Laboratories, West Grove, Pa.) at 5 μg/mL in PBS, and 100 μL/well in 96-well plates (Nunc-Immuno plate Maxisorp). Coated plates were covered and incubated at 4° C. overnight. Plates then were washed 4 times with 0.05% Tween (Tween 20) in PBS, and blocked with 1% BSA/1% goat serum in PBS, 200 μL/well. After incubation with the blocking buffer at 37° C. for 2 hrs, the plates were washed 4 times with 0.05% Tween in PBS and tapped dry on paper towels.

B. Incubation with Test Samples and Secondary Antibody

Test samples were diluted as appropriate in sample buffer (1% BSA/1% goat serum/0.05% Tween in PBS). A standard curve was prepared using a chimeric antibody (with a human Fc), the concentration of which was known. To prepare a standard curve, serial dilutions were made in the sample buffer to give a standard curve ranging from 125 ng/mL to 3.9 ng/mL. The diluted samples and standards were added to the plate, 100 μL/well and the plate incubated at 37° C. for 2 hr. After incubation, the plate was washed 8 times with 0.05% Tween in PBS. To each well was then added 100 μL of the secondary antibody, the horseradish peroxidase-conjugated anti-human IgG (Jackson Immuno Research), diluted around 1:120,000 in the sample buffer. The exact dilution of the secondary antibody has to be determined for each lot of the HRP-conjugated anti-human IgG. After incubation at 37° C. for 2 hr, the plate was washed 8 times with 0.05% Tween in PBS.

C. Development

The substrate solution was added to the plate at 100 μL/well. The substrate solution was prepared by dissolving 30 mg of OPD (o-phenylenediamine dihydrochloride (OPD), (1 tablet) into 15 mL of 0.025 M Citric acid/0.05 M Na2HPO4 buffer, pH 5, which contained 0.03% of freshly added hydrogen peroxide. The color was allowed to develop for 30 min. at room temperature in the dark. The developing time is subject to change, depending on lot to lot variability of the coated plates, the secondary antibody, etc. The reaction was stopped by adding 4N sulfuric acid, 100 μL/well. The plate was read by a plate reader, which was set at both 490 and 650 nm and programmed to subtract the background OD at 650 nm from the OD at 490 nm.

Example 5 Purification and Analysis of huFc-IFN-β Proteins

A standard purification of Fc-containing fusion proteins was performed based on the affinity of the Fc protein moiety for Protein A. Briefly, cell supernatants (from cells transfected with wildtype or mutant proteins) containing the fusion protein were loaded onto a pre-equilibrated (50 mM Sodium Phosphate, 150 mM NaCl at neutral pH) Protein A Sepharose Fast Flow column and the column was washed extensively in buffer (50 mM Sodium Phosphate, 150 mM NaCl at neutral pH). Bound protein was eluted at a low pH (pH 2.5) in same buffer as above and fractions were immediately neutralized, optionally by eluting directly into a solution of 1M Tris base, pH 11.

The Protein A Sepharose—purified huFc-IFN-β and huFc-IFN-β^(sol) fusion proteins were analyzed by analytical size exclusion chromatography (SEC), and the % non-aggregated material was quantified by calculating the area under the curve of chromatogram peaks. The integrity and purity of the fusion proteins was verified by SDS-PAGE electrophoresis.

TABLE 1 Analytical SEC analysis of Fc-IFN-β fusion proteins Protein % non-aggregated Fc-γ4h-IFN-β  0 Fc-γ4h-IFN-β(C17S) 11 Fc-γ4h-linker-IFN-β(C17S) 21-30 Fc-γ4h-linker-IFN-β(C17S F50H H131A H140A) 52 Fc-γ4h-linker-IFN-β(C17S L57A H131A H140T) 49

In a second purification step, neutralized Protein A Sepharose eluates containing Fc-IFN-β^(sol) fusion proteins were applied to a preparative SEC column and peak fractions were collected, yielding Fc-IFN-β^(sol) protein preparations consisting of at least 90% non-aggregated material. While the yield of purified product for Fc-γ4h-linker-IFN-β(C17S) was about 10%, for Fc-γ4h-linker-IFN-β^(sol)(C17S L57A H131A H140T) it was about 75%. This result indicated that the combination of mutations C17S with, for example L57A, H131A, and H140T in the IFN-β moiety significantly promoted the solubility characteristics of the Fc-IFN-β fusion proteins.

Example 6 Measurement of Antiviral Activity

Viral replication in cell culture often results in cytotoxicity, an effect known as cytopathic effect (CPE). Interferons can inhibit viral proliferation and protect cells from CPE. The antiviral activity of IFN-β can be quantitated by cytopathic effect reduction (CPER), as described in “Lymphokines and Interferons: A Practical Approach”, edited by M. J. Clemens, A. G. Morris, and A. J. H. Gearin, I. R. L. Press, Oxford, 1987. The antiviral activities of purified huFc-IFN-β and huFc-IFN-β^(sol) were compared relative to a commercial huIFN-β standard (R&D Systems) or Betaferon (Serono) using the human epithelial lung carcinoma line A549 (ATCC # CCL-185) and the encephalomyocarditis virus (EMCV; ATCC # VR 129B) according to the CPER protocol described in the above reference. The effective dose (ED50) was set as the amount of protein that led to 50% CPER (i.e. 50% of the cells being protected from lysis), determined relative to uninfected control cells. The ED50 values were the average of at least three separate experiments. It was found that the effective doses that gave 50% CPER were 50 pg/ml for huFc-IFN-β 70 pg/ml for huFc-IFN-β^(sol)(C17S), 14 pg/ml for huFc-IFN-β^(sol)(C17S, F50H, H131A, H140A) and 17 pg/ml for huFc-IFN-β^(sol)(C17S, L57A, H131A, H140T). These values, which had been normalized to the amount of IFN-β in the fusion protein, correlated well with the ED50 of 90 pg/ml or 40 pg/ml found with the commercial standard or Betaferon, respectively. Therefore, the IFN-β fusion proteins retained substantial anti-viral activity in a CPER assay, and the huFc-IFN-β^(sol) fusion proteins had an ED50 about equivalent to that of the free huIFN-β.

Example 7 Cellular Growth Inhibition Assay

The activity of the purified Fc-IFN-β fusion proteins was further determined in a cellular growth inhibition assay. The proliferation of Daudi cells (ATCC # CCL-123), a B lymphoblast line derived from a patient with Burkitt's lymphoma, is normally inhibited by IFN-β. Accordingly, the antiproliferative effects of fusion proteins huFc-IFN-β and huFc-IFN-β^(sol)(C17S) on Daudi cells were compared relative to a commercial human standard (Calbiochem). To set up the assay for each of these proteins, a dilution series covering about a thousand fold concentration range was prepared in RPMI medium supplemented with 10% fetal bovine serum, and 100 μl samples were aliquoted in wells of a 96 well plate. Daudi cells in growth phase were washed and resuspended at 2×10⁵ cells/ml in the RPMI medium supplemented with 10% fetal bovine serum, and 100 μl of the cells were aliquoted to each well containing the IFN-β dilutions. Further control wells contained either untreated cells or medium alone. After incubation for an additional 72 hours proliferation was measured by mitochondrial dehydrogenase activity, using the chromogenic enzyme substrate MTS (Promega # G5421) in the presence of the electron donor PMS (Sigma # P 5812). The ED50 values, determined from activity curves, were found to be around 3 ng/ml to 3.5 ng/ml for each of the fusion proteins as well as for the commercial IFN-β protein. It was therefore concluded that the IFN-β fusion proteins were as effective as the free IFN-β in inhibiting Daudi cell growth.

Example 8 Pharmacokinetics of huFc-IFN-β Proteins

The pharmacokinetics of huFc-IFN-β and huFc-IFN-β^(sol) fusion proteins are determined in a group of 4 Balb/c mice, for each protein. Twenty-five milligrams of the fusion protein is injected into the tail vein of each mouse. Blood is obtained by retro-orbital bleeding immediately after injection (i.e., at t=0 min), and at 30 min, 1 hr, 2 hrs, 4 hrs, 8 hrs, and 24 hrs post-injection. Blood samples are collected in tubes containing heparin to prevent clotting. Cells are removed by centrifugation in an Eppendorf high-speed microcentrifuge for 4 min at 12,500 g. The concentration of either Fc-huIFN-β or huFc-IFN-β^(sol) in the plasma is measured by anti-huFc ELISA and Western blot analysis using anti-huFc antibody. Alternatively, an IFN-β ELISA may be used. The integrity of the circulating fusion protein is ascertained by an immunoblot of the serum probed with an anti-huFc antibody or with an anti-IFN-β antibody. It is found that the circulating half-life of huFc-IFN-β^(sol) is greater than that of huFc-IFN-β, and at least 5-fold that of the free IFN-β.

Furthermore, it is contemplated that the specific effects of Fc-IFN-β^(sol) are more pronounced in treatment of conditions and diseases such as multiple sclerosis, where administration of IFN-β is known to alleviate the condition.

EQUIVALENTS

The invention may be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are therefore to be considered in all respects illustrative rather than limiting on the invention described herein. The scope of the invention is thus indicated by the appended claims rather than by the foregoing description. All changes which come within the meaning and range of equivalency of the claims are therefore intended to be embraced therein. 

1-22. (canceled)
 23. A method of stabilizing an Fc-interferon-β fusion protein comprising the step of making an Fc-interferon-β fusion protein, the Fc-interferon-β fusion protein comprising: an immunoglobulin Fc region; and a human interferon-β protein linked by a peptide bond or a peptide linker sequence to the carboxy-terminus of the immunoglobulin Fc region, wherein the interferon-β protein comprises SEQ ID NO: 2 with at least two substitutions selected from the group consisting of C17S, C17A, C17V, C17M, F50H, L57A, L130A, H131A, K136A, H140A, and H140T.
 24. The method of claim 1, wherein the immunoglobulin Fc region comprises an immunoglobulin hinge region and an immunoglobulin heavy chain constant region.
 25. The method of claim 1, wherein the immunoglobulin Fc region is derived from IgG4, IgG2, IgG1, or a combination thereof.
 26. The method of claim 3, wherein the immunoglobulin heavy chain constant region is derived from IgG4 and the immunoglobulin hinge region is derived from IgG1.
 27. The method of claim 4, wherein a cysteine residue of the hinge region has been mutated.
 28. The method of claim 3, wherein the immunoglobulin Fc region is derived from IgG1, and an alanine residue is substituted in place of a C-terminal lysine of the immunoglobulin Fc region.
 29. The method of claim 3, wherein the immunoglobulin heavy chain constant region is derived from IgG2, and the immunoglobulin hinge region is derived from IgG1.
 30. The method of claim 7, wherein a cysteine residue of the hinge region has been mutated.
 31. The method of claim 3, wherein the immunoglobulin Fc region is derived from IgG2, and an alanine residue is substituted in place of the C-terminal lysine of the immunoglobulin Fc region.
 32. The method of claim 1, wherein the human interferon-β protein is linked to the carboxy-terminus of the immunoglobulin Fc region by peptide linker sequence Gly₄SerGly₄SerGly₃SerGly (SEQ ID NO:1).
 33. The method of claim 1, wherein the interferon-β protein has the following amino acid substitutions: C17S and F50H and H131A and H140T or H140A; or C17S and L57A and H131A and H140T or H140A.
 34. The method of claim 1, wherein the immunoglobulin Fc region comprises IgG1, IgG2, or IgG4.
 35. The method of claim 1, wherein the immunoglobulin Fc region comprises IgG4 and at least a portion of a hinge of IgG1.
 36. The method of claim 1, wherein said fusion protein comprises the amino acid sequence of SEQ ID NO:
 8. 37. The method of claim 1, wherein stabilizing comprises: (i) increasing the circulating half-life of the Fc-interferon-β fusion protein relative to an unaltered Fc-interferon-β fusion protein, or (ii) decreasing the aggregation of the Fc-interferon-β fusion protein relative to an unaltered Fc-interferon-β fusion protein, or (iii) increasing the biological activity of the Fc-interferon-β fusion protein relative to an unaltered Fc-interferon-β fusion protein.
 38. A method of treating a patient for a condition alleviated by the administration of interferon-β comprising the step of administering an effective amount of an Fc-interferon-β fusion protein to a mammal having the condition, wherein the Fc-interferon-β fusion protein comprises: an immunoglobulin Fc region; and a human interferon-β protein linked by a peptide bond or a peptide linker sequence to the carboxy-terminus of the immunoglobulin Fc region, wherein the interferon-β protein comprises SEQ ID NO: 2 with at least two substitutions selected from the group consisting of C17S, C17A, C17V, C17M, F50H, L57A, L130A, H131A, K136A, H140A, and H140T. 